Contact experts in Gromacs to get answers
1,330 views 1,449 posts
Questions related to Gromacs
1. I am processing my umbrella sampling simulations using the Weighted Histogram Analysis Method in Gromacs (gmx wham). However, I would like to report the mean dG and a standard deviation. To do...
16 March 2020 1,567 3 View
Hi, I am familiar with performing MD simulations using Gromacs on protein-ligand complexes. However, BAR is a new technique to me and I need specific clarification of the decoupling sequence...
13 March 2020 3,724 1 View
I know that the change from Gromacs 4 to 5 changed quite a few things, but I believe gromacs is set up to be backwards compatible am afraid that I do not know what the settings that would need to...
11 March 2020 3,792 2 View
I am trying to simulation protein in non-aqueous solvents and I put my protein in MeOH with Charmm36 force field. After I tried to minimize the energy. it gives: Energy minimization has stopped,...
07 March 2020 8,326 3 View
Can anyone tell me how to estimate the turning movements at roundabouts with only counting the entry volumes at each approach? A generalizes equation or model to do that, or a prepared spreadsheet.
01 March 2020 5,211 0 View
Hello everyone, I have to do molecular dynamics of a metalloprotein. I have read in literature that we can use the CHARMM force field in Gromacs for metal protein. Beside CHARMM I also use...
28 February 2020 9,905 6 View
Hello everyone, I'm new to gromacs and also new to umbrella sampling, so I'm following Justin's tutorial http://www.mdtutorials.com/gmx/umbrella/index.html ; On the umbrella sampling stage, I'm...
21 February 2020 1,852 3 View
Hi everyone, I want to change the segid name of topology(in pdb format) and gromacs trajectory. To later generate a new topology and trajectory with the changed names. Do you know a way to do...
17 February 2020 2,983 1 View
I want to know how to fix the separation of 2 chains after the production run. I'm trying different combinations of trajconv after creating an index file having a specific residue(s) on the...
13 February 2020 1,912 2 View
I am currently working on a system that contains a DMPG bilayer with amyloid beta monomer on one side of the membrane. I generated the system using CHARMM-GUI and oriented the protein using the...
02 February 2020 10,132 1 View
In theory, dH/dL (or dV/dL in thermodynamic integration) originated from the difference in enthalpies of two distinct states lambda and lambda+dL. I wonder how the Gromacs module calculates the...
02 February 2020 3,929 1 View
02 February 2020 3,890 3 View
Dear Gromacs users I am trying to make a system with 1 single amino acid(PHE) and 1 Ligand when I run pdb2gmx it gives me error:- Fatal error: In the chosen force field there is no residue type...
02 February 2020 4,731 3 View
Hi! Does anyone know if its possible to get sub-pm resolution in the lets say dist.xvg file produced with gmx distance when analyzing a Gromacs .trr trajectory? Hence, instead of seeing...
02 February 2020 873 2 View
02 February 2020 8,967 1 View
02 February 2020 9,756 1 View
Hi! May I please ask for your help to see how to fix the following problem? When I use software package GROMACS in phoenix with following command: python cgenff_charmm2gmx_py3_nx2.py JZ4...
02 February 2020 1,722 2 View
I am trying to simulate a complex consisting of DNA and a protein using Gromacs. One chain is methylated at C. The methylated cytosine is included in the newest Charmm36 forcefield as D5MC, yet...
02 February 2020 5,327 1 View
I am trying to define a new residue to AMBER forcefield in gromacs. pdb2gmx is giving "missing atoms" error (All atoms are reported as missing) when I define all the hydrogens in the .rtp file...
02 February 2020 5,201 3 View
Hi all, Currently I am working with CG- Mie potentials and I have obtained good results, but option clustsize doesn't work well for me after simulation. I think that the problem could be in the...
02 February 2020 7,714 3 View
02 February 2020 324 5 View
I am working on imaging a fluorescent protein expressed in HEK293-T cells with 2-photon excitation for long time durations (1-2 hours). I notice movement and changes in morphology of the cells...
28 January 2020 1,209 2 View
HI All, "ERROR : No.of Coordinates in Solv.gro and Topol.top not matching" I am trying to run GROMACS simulation for Protein-Ligand complex, and I am facing this issue, and I dont know how to...
23 January 2020 4,991 3 View
Hello everyone, I'm running MMPBSA by using the g_mmpbsa tool for GROMACS. However, it runs extremely slow even though it's claimed that by default it uses all the processors:...
21 January 2020 1,021 1 View